Grand Fir / Snowbrush Microbiome

2024-03-05

Preliminary data exploration

Contaminant ASVs were identified with the prevalence method using the decontam package.

Plant measures overview

Scaled-centered plant ‘health’ measures, broken down by treatment factors.

Figure 1

Model output

Formula: value ~ drought * host * site + (1|block))

Table 1
effect term estimate std.error statistic df p.value
fixed (Intercept) 0.071 0.280 0.255 5.343 0.808
fixed droughtND -0.017 0.163 -0.106 384.262 0.916
fixed hostCeanothus velutinus -0.522 0.164 -3.190 381.647 0.002
fixed fire_freq 0.104 0.154 0.675 5.360 0.528
fixed droughtND:hostCeanothus velutinus 0.560 0.232 2.412 383.262 0.016
fixed droughtND:fire_freq -0.037 0.089 -0.416 381.323 0.677
fixed hostCeanothus velutinus:fire_freq -0.002 0.090 -0.017 382.464 0.987
fixed droughtND:hostCeanothus velutinus:fire_freq -0.033 0.127 -0.263 382.083 0.793



Inoculum communities overview

Taxonomic overview

Bacteria

Figure 2

Alpha diversity

Effect of Shannon diversity on plant measures

## overall_transformed_plant_value ~ Shannon * host * drought * 
##     inoculum_site + (1 | block)
## <environment: 0x55ebcea9f370>

Table 2

effect group term estimate std.error statistic df p.value
fixed NA (Intercept) -1.226 0.507 -2.417 122.238 0.017
fixed NA Shannon 0.301 0.101 2.993 609.763 0.003
fixed NA hostCeanothus velutinus 0.984 2.559 0.385 610.106 0.701
fixed NA droughtND -0.187 2.351 -0.079 609.423 0.937
fixed NA inoculum_site2 1.378 1.915 0.720 609.868 0.472
fixed NA inoculum_site3 1.749 4.502 0.389 610.099 0.698
fixed NA inoculum_site4 1.827 1.868 0.978 610.007 0.328
fixed NA inoculum_site5 6.697 3.448 1.942 609.951 0.053
fixed NA inoculum_site6 6.414 1.849 3.470 610.406 0.001
fixed NA inoculum_siteSterile 7.260 2.633 2.757 609.891 0.006
fixed NA Shannon:hostCeanothus velutinus -0.301 0.424 -0.709 610.132 0.478
fixed NA Shannon:droughtND -0.033 0.409 -0.080 609.263 0.936
fixed NA hostCeanothus velutinus:droughtND 17.677 8.477 2.085 611.147 0.037
fixed NA Shannon:inoculum_site2 -0.223 0.345 -0.647 609.967 0.518
fixed NA Shannon:inoculum_site3 -0.477 0.754 -0.633 610.113 0.527
fixed NA Shannon:inoculum_site4 -0.334 0.352 -0.948 610.051 0.344
fixed NA Shannon:inoculum_site5 -1.150 0.612 -1.879 609.963 0.061
fixed NA Shannon:inoculum_site6 -1.153 0.330 -3.495 610.521 0.001
fixed NA Shannon:inoculum_siteSterile -1.391 0.457 -3.045 609.950 0.002
fixed NA hostCeanothus velutinus:inoculum_site2 -1.457 3.239 -0.450 610.782 0.653
fixed NA hostCeanothus velutinus:inoculum_site3 -2.040 6.432 -0.317 611.675 0.751
fixed NA hostCeanothus velutinus:inoculum_site4 -5.726 4.534 -1.263 610.573 0.207
fixed NA hostCeanothus velutinus:inoculum_site5 -9.239 6.982 -1.323 610.067 0.186
fixed NA hostCeanothus velutinus:inoculum_site6 -16.444 7.791 -2.111 608.880 0.035
fixed NA hostCeanothus velutinus:inoculum_siteSterile -7.195 4.427 -1.625 611.688 0.105
fixed NA droughtND:inoculum_site2 -1.482 3.252 -0.456 608.582 0.649
fixed NA droughtND:inoculum_site3 1.646 5.810 0.283 615.792 0.777
fixed NA droughtND:inoculum_site4 2.497 3.822 0.653 609.716 0.514
fixed NA droughtND:inoculum_site5 -2.968 4.505 -0.659 609.380 0.510
fixed NA droughtND:inoculum_site6 -3.067 3.816 -0.804 609.535 0.422
fixed NA droughtND:inoculum_siteSterile -5.102 4.529 -1.127 608.940 0.260
fixed NA Shannon:hostCeanothus velutinus:droughtND -2.903 1.447 -2.007 611.120 0.045
fixed NA Shannon:hostCeanothus velutinus:inoculum_site2 0.265 0.551 0.481 610.838 0.631
fixed NA Shannon:hostCeanothus velutinus:inoculum_site3 0.467 1.042 0.448 611.699 0.654
fixed NA Shannon:hostCeanothus velutinus:inoculum_site4 1.033 0.764 1.352 610.587 0.177
fixed NA Shannon:hostCeanothus velutinus:inoculum_site5 1.626 1.148 1.416 610.110 0.157
fixed NA Shannon:hostCeanothus velutinus:inoculum_site6 2.803 1.253 2.237 608.849 0.026
fixed NA Shannon:hostCeanothus velutinus:inoculum_siteSterile 1.380 0.739 1.868 611.677 0.062
fixed NA Shannon:droughtND:inoculum_site2 0.315 0.576 0.546 608.588 0.585
fixed NA Shannon:droughtND:inoculum_site3 -0.280 0.990 -0.283 615.999 0.777
fixed NA Shannon:droughtND:inoculum_site4 -0.250 0.673 -0.372 609.580 0.710
fixed NA Shannon:droughtND:inoculum_site5 0.562 0.795 0.706 609.339 0.480
fixed NA Shannon:droughtND:inoculum_site6 0.615 0.686 0.897 609.495 0.370
fixed NA Shannon:droughtND:inoculum_siteSterile 1.016 0.779 1.304 608.901 0.193
fixed NA hostCeanothus velutinus:droughtND:inoculum_site2 -13.825 9.008 -1.535 610.965 0.125
fixed NA hostCeanothus velutinus:droughtND:inoculum_site3 -23.837 11.167 -2.135 614.160 0.033
fixed NA hostCeanothus velutinus:droughtND:inoculum_site4 -12.860 9.807 -1.311 610.900 0.190
fixed NA hostCeanothus velutinus:droughtND:inoculum_site5 -6.875 11.623 -0.591 609.219 0.554
fixed NA hostCeanothus velutinus:droughtND:inoculum_site6 1.508 11.603 0.130 609.041 0.897
fixed NA hostCeanothus velutinus:droughtND:inoculum_siteSterile -11.042 9.889 -1.117 610.051 0.265
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site2 2.325 1.546 1.503 610.908 0.133
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site3 4.032 1.880 2.145 614.514 0.032
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site4 2.020 1.678 1.204 610.839 0.229
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site5 1.194 1.944 0.614 609.262 0.539
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site6 -0.260 1.938 -0.134 609.046 0.893
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_siteSterile 1.757 1.684 1.044 609.997 0.297
ran_pars block sd__(Intercept) 0.537 NA NA NA NA
ran_pars Residual sd__Observation 0.812 NA NA NA NA

Fungi

Figure 3

Alpha diversity

Effect of Shannon diversity on plant measures

Table 3 

## overall_transformed_plant_value ~ Shannon * host * drought * 
##     inoculum_site + (1 | block)
## <environment: 0x55ebcea9f370>
effect group term estimate std.error statistic df p.value
fixed NA (Intercept) 0.849 0.357 2.379 175.175 0.018
fixed NA Shannon -0.494 0.187 -2.639 781.982 0.008
fixed NA hostCeanothus velutinus -0.898 0.731 -1.228 781.153 0.220
fixed NA droughtND -0.100 0.586 -0.170 780.300 0.865
fixed NA inoculum_site2 -0.307 0.780 -0.394 780.746 0.694
fixed NA inoculum_site3 -0.923 0.625 -1.478 782.135 0.140
fixed NA inoculum_site4 -0.526 0.439 -1.199 778.320 0.231
fixed NA inoculum_site5 -0.416 0.899 -0.463 779.825 0.644
fixed NA inoculum_site6 1.264 0.950 1.330 781.558 0.184
fixed NA inoculum_siteSterile -0.601 0.835 -0.720 779.664 0.472
fixed NA Shannon:hostCeanothus velutinus 0.253 0.368 0.686 781.374 0.493
fixed NA Shannon:droughtND 0.071 0.391 0.182 780.743 0.856
fixed NA hostCeanothus velutinus:droughtND 0.423 1.009 0.419 779.046 0.676
fixed NA Shannon:inoculum_site2 0.464 0.412 1.127 780.882 0.260
fixed NA Shannon:inoculum_site3 0.286 0.407 0.703 782.551 0.482
fixed NA Shannon:inoculum_site4 0.472 0.272 1.733 778.563 0.084
fixed NA Shannon:inoculum_site5 0.561 0.521 1.077 779.847 0.282
fixed NA Shannon:inoculum_site6 -0.426 0.463 -0.921 781.844 0.357
fixed NA Shannon:inoculum_siteSterile 0.148 0.573 0.259 779.993 0.796
fixed NA hostCeanothus velutinus:inoculum_site2 -1.597 1.728 -0.924 783.189 0.356
fixed NA hostCeanothus velutinus:inoculum_site3 1.317 1.087 1.212 779.267 0.226
fixed NA hostCeanothus velutinus:inoculum_site4 1.081 1.230 0.879 780.948 0.379
fixed NA hostCeanothus velutinus:inoculum_site5 0.875 1.388 0.630 778.872 0.529
fixed NA hostCeanothus velutinus:inoculum_site6 -1.300 1.398 -0.930 779.092 0.353
fixed NA hostCeanothus velutinus:inoculum_siteSterile 3.604 2.018 1.786 782.650 0.074
fixed NA droughtND:inoculum_site2 -0.134 1.054 -0.128 778.928 0.899
fixed NA droughtND:inoculum_site3 -0.704 0.936 -0.752 783.662 0.452
fixed NA droughtND:inoculum_site4 0.278 0.730 0.381 779.650 0.703
fixed NA droughtND:inoculum_site5 1.726 1.308 1.320 779.211 0.187
fixed NA droughtND:inoculum_site6 -1.982 1.176 -1.686 781.343 0.092
fixed NA droughtND:inoculum_siteSterile -0.932 1.574 -0.592 779.049 0.554
fixed NA Shannon:hostCeanothus velutinus:droughtND 0.107 0.564 0.189 779.603 0.850
fixed NA Shannon:hostCeanothus velutinus:inoculum_site2 0.401 0.759 0.529 783.178 0.597
fixed NA Shannon:hostCeanothus velutinus:inoculum_site3 -0.635 0.624 -1.017 779.000 0.309
fixed NA Shannon:hostCeanothus velutinus:inoculum_site4 -0.621 0.606 -1.025 781.143 0.306
fixed NA Shannon:hostCeanothus velutinus:inoculum_site5 -0.621 0.703 -0.883 779.016 0.377
fixed NA Shannon:hostCeanothus velutinus:inoculum_site6 0.524 0.674 0.778 779.068 0.437
fixed NA Shannon:hostCeanothus velutinus:inoculum_siteSterile -2.208 1.304 -1.693 782.565 0.091
fixed NA Shannon:droughtND:inoculum_site2 0.018 0.642 0.028 779.055 0.978
fixed NA Shannon:droughtND:inoculum_site3 0.468 0.656 0.713 761.413 0.476
fixed NA Shannon:droughtND:inoculum_site4 0.336 0.516 0.651 780.553 0.515
fixed NA Shannon:droughtND:inoculum_site5 -1.160 0.814 -1.425 779.215 0.155
fixed NA Shannon:droughtND:inoculum_site6 1.144 0.662 1.729 781.593 0.084
fixed NA Shannon:droughtND:inoculum_siteSterile 1.043 1.199 0.870 779.158 0.384
fixed NA hostCeanothus velutinus:droughtND:inoculum_site2 3.098 2.246 1.379 783.493 0.168
fixed NA hostCeanothus velutinus:droughtND:inoculum_site3 0.031 1.488 0.021 782.971 0.984
fixed NA hostCeanothus velutinus:droughtND:inoculum_site4 -0.831 1.480 -0.561 780.610 0.575
fixed NA hostCeanothus velutinus:droughtND:inoculum_site5 -2.121 1.903 -1.114 781.010 0.265
fixed NA hostCeanothus velutinus:droughtND:inoculum_site6 1.765 1.935 0.912 779.142 0.362
fixed NA hostCeanothus velutinus:droughtND:inoculum_siteSterile -2.625 2.547 -1.031 780.772 0.303
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site2 -1.282 1.099 -1.166 783.243 0.244
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site3 -0.417 1.000 -0.417 782.862 0.677
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site4 -0.040 0.805 -0.050 781.159 0.960
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site5 1.334 1.075 1.240 781.134 0.215
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site6 -1.164 1.046 -1.113 778.965 0.266
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_siteSterile 1.589 1.822 0.872 780.899 0.384
ran_pars block sd__(Intercept) 0.339 NA NA NA NA
ran_pars Residual sd__Observation 0.879 NA NA NA NA

AMF

Figure 4

Alpha diversity

Effect of Shannon diversity on plant measures

Table 4 

## overall_transformed_plant_value ~ Shannon * host * drought * 
##     inoculum_site + (1 | block)
## <environment: 0x55ebcea9f370>
effect group term estimate std.error statistic df p.value
fixed NA (Intercept) -0.774 0.228 -3.399 342 0.001
fixed NA Shannon 0.234 0.159 1.469 342 0.143
fixed NA droughtND 0.975 0.351 2.778 342 0.006
fixed NA inoculum_site1 0.079 0.438 0.182 342 0.856
fixed NA inoculum_site2 1.292 0.612 2.111 342 0.036
fixed NA inoculum_site3 0.070 0.467 0.150 342 0.881
fixed NA inoculum_site4 0.465 0.334 1.389 342 0.166
fixed NA inoculum_site5 0.680 0.588 1.157 342 0.248
fixed NA inoculum_site6 0.413 0.535 0.773 342 0.440
fixed NA Shannon:droughtND -0.151 0.222 -0.677 342 0.499
fixed NA Shannon:inoculum_site1 -0.150 0.271 -0.552 342 0.581
fixed NA Shannon:inoculum_site2 -0.579 0.297 -1.945 342 0.053
fixed NA Shannon:inoculum_site3 -0.152 0.259 -0.586 342 0.558
fixed NA Shannon:inoculum_site4 -0.238 0.227 -1.045 342 0.297
fixed NA Shannon:inoculum_site5 -0.321 0.328 -0.976 342 0.330
fixed NA Shannon:inoculum_site6 -0.258 0.295 -0.876 342 0.382
fixed NA droughtND:inoculum_site1 0.288 0.651 0.443 342 0.658
fixed NA droughtND:inoculum_site2 -1.133 1.025 -1.105 342 0.270
fixed NA droughtND:inoculum_site3 -0.941 0.592 -1.588 342 0.113
fixed NA droughtND:inoculum_site4 -0.362 0.581 -0.623 342 0.534
fixed NA droughtND:inoculum_site5 1.175 1.236 0.951 342 0.342
fixed NA droughtND:inoculum_site6 -0.880 0.740 -1.190 342 0.235
fixed NA Shannon:droughtND:inoculum_site1 0.013 0.358 0.035 342 0.972
fixed NA Shannon:droughtND:inoculum_site2 0.577 0.445 1.298 342 0.195
fixed NA Shannon:droughtND:inoculum_site3 0.346 0.335 1.030 342 0.304
fixed NA Shannon:droughtND:inoculum_site4 0.290 0.334 0.867 342 0.386
fixed NA Shannon:droughtND:inoculum_site5 -0.365 0.555 -0.658 342 0.511
fixed NA Shannon:droughtND:inoculum_site6 0.506 0.389 1.302 342 0.194
ran_pars block sd__(Intercept) 0.000 NA NA NA NA
ran_pars Residual sd__Observation 0.912 NA NA NA NA

Comparison between inoculum and root communities

Bacteria

Figure 5

Figure 6


Not all taxa in the inoculae were subsequently found in the root samples

Figure 7


Fungi

Figure 8

Figure 9


Not all taxa in the inoculae were subsequently found in the root samples

Figure 10


AMF

Figure 11

Figure 12
Not all taxa in the inoculae were subsequently found in the root samples

Figure 13



Microbial guilds

Bacteria

I couldn’t get a trustworthy annotation of “mutualists” for bacteria, but here are probable pathogens:

Figure 14

Table 5

## value ~ proportion_pathogen * drought + (1 | block)
## <environment: 0x55ebc7f95920>
effect term estimate std.error statistic df p.value species
fixed (Intercept) -0.4579 0.2353 -1.9458 27.6894 0.0619 Ceanothus
fixed proportion_pathogen 0.1621 0.5053 0.3209 480.8904 0.7484 Ceanothus
fixed droughtND 1.5430 0.2479 6.2243 477.2195 0.0000 Ceanothus
fixed proportion_pathogen:droughtND -2.3112 0.6993 -3.3049 477.2112 0.0010 Ceanothus
fixed (Intercept) -0.3939 0.2931 -1.3441 25.3702 0.1908 Abies
fixed proportion_pathogen 1.0819 0.7509 1.4409 572.5931 0.1502 Abies
fixed droughtND 0.6770 0.3000 2.2564 575.5163 0.0244 Abies
fixed proportion_pathogen:droughtND -1.8231 0.9838 -1.8530 574.8925 0.0644 Abies

Fungi

How does the proportion of mutualist fungi relate to indicators of plant health?

In the following figure, the X-axis represents the proportion of fungi that could be identified to a mutualistic guild; the Y-axis represents the value of the various measures of plant success (facets). Y-axis scales vary between facets.

Figure 15

We see an opposite pattern when looking at the proportions of putatively pathogenic fungi

Figure 16

Table 6
effect term estimate std.error statistic df p.value species
fixed (Intercept) -0.3848 0.1554 -2.4770 10.3000 0.0321 Ceanothus
fixed proportion_pathogen -0.0762 0.3574 -0.2132 481.0062 0.8313 Ceanothus
fixed droughtND 0.6753 0.1250 5.4009 478.1959 0.0000 Ceanothus
fixed proportion_pathogen:droughtND 0.4287 0.4150 1.0329 479.3019 0.3022 Ceanothus
fixed (Intercept) -0.0688 0.2101 -0.3274 7.1524 0.7527 Abies
fixed proportion_pathogen -0.1814 0.2844 -0.6379 573.1111 0.5238 Abies
fixed droughtND 0.1921 0.0886 2.1688 573.6082 0.0305 Abies
fixed proportion_pathogen:droughtND -0.6108 0.4253 -1.4363 573.5218 0.1515 Abies
fixed (Intercept) -0.3742 0.1503 -2.4889 9.9940 0.0321 Ceanothus
fixed proportion_mutualist -0.0827 0.2166 -0.3819 479.6347 0.7027 Ceanothus
fixed droughtND 0.6036 0.1276 4.7314 478.5951 0.0000 Ceanothus
fixed proportion_mutualist:droughtND 0.4942 0.2831 1.7455 479.6174 0.0815 Ceanothus
fixed (Intercept) -0.2483 0.2112 -1.1758 8.3423 0.2722 Abies
fixed proportion_mutualist 0.3212 0.1589 2.0218 573.6672 0.0437 Abies
fixed droughtND -0.0055 0.1256 -0.0441 573.6806 0.9648 Abies
fixed proportion_mutualist:droughtND 0.2734 0.2233 1.2241 575.2517 0.2214 Abies



Beta-Diversity

Bacteria

Figure 17

Table 7

## PermANOVA run without outlier Sterile-inoculum root samples...
term df SumOfSqs R2 statistic p.value
host 1 3.8414120 0.0687480 12.836684 0.001
inoculum_site 5 7.1862718 0.1286094 4.802812 0.001
drought 1 0.8088162 0.0144750 2.702787 0.001
host:inoculum_site 5 3.6135887 0.0646707 2.415075 0.001
host:drought 1 0.7562988 0.0135351 2.527292 0.001
inoculum_site:drought 5 1.9283329 0.0345105 1.288766 0.005
host:inoculum_site:drought 5 1.8316856 0.0327808 1.224173 0.018
Residual 120 35.9103196 0.6426704 NA NA
Total 143 55.8767255 1.0000000 NA NA

Fungi

Figure 18

Table 7

## PermANOVA run without outlier Sterile-inoculum root samples...
term df SumOfSqs R2 statistic p.value
host 1 1.8555637 0.0288094 5.687460 0.001
inoculum_site 5 14.1030579 0.2189636 8.645414 0.001
drought 1 0.6383236 0.0099106 1.956516 0.007
host:inoculum_site 5 4.4734164 0.0694541 2.742280 0.001
host:drought 1 0.4690934 0.0072831 1.437811 0.082
inoculum_site:drought 5 2.0071801 0.0311634 1.230436 0.052
host:inoculum_site:drought 5 1.7109789 0.0265646 1.048859 0.351
Residual 120 39.1506299 0.6078512 NA NA
Total 143 64.4082440 1.0000000 NA NA

AMF

Figure 19

Table 8

## PermANOVA run without outlier Sterile-inoculum root samples...
term df SumOfSqs R2 statistic p.value
inoculum_site 6 6.9907731 0.2129210 2.9819777 0.001
drought 1 0.3007071 0.0091588 0.7696159 0.777
inoculum_site:drought 6 2.0978089 0.0638939 0.8948394 0.770
Residual 60 23.4434120 0.7140263 NA NA
Total 73 32.8327011 1.0000000 NA NA



Important Taxa

These taxa were identified by both Random Forest models and corncob as being important predictors of the various experimental conditions & had significant differential abundance between levels of those variables

Bacteria

Differential Abundance

Figure 20

Relative Abundances of ‘important’ taxa in root samples

Figure 21

Fungi

Differential Abundance

Figure 22

No fungal taxa were found to have significant differential abundance between drought levels

Relative Abundances of ‘important’ taxa in root samples

Figure 23


AMF

Differential Abundance

Figure 24

No fungal taxa were found to have significant differential abundance between drought levels

Relative Abundances of ‘important’ taxa in root samples

Figure 25



Phylogenetic properties

Bacteria

  • Still kind of messy
  • What specific questions do we need to address with this?

Fungi

  • Phylogenetic dispersion is tricky with ITS markers :(
  • Could try GhostTree for fungi of interest that come up as ‘unknown’



Network properties

Selected network attributes

Figure 26

Network properties vs Plant Health

(Composite scaled-centered plant health measures)

Table 9

## plant_health_indicator ~ species * kingdom * (n_vertices + n_edges + 
##     mean_dist + mean_betweenness + mean_closeness + global_effic + 
##     clustering_coeficient + max_degree)
Table 10
term estimate std.error statistic p.value
(Intercept) -0.3395498 1.1487865 -0.2955726 0.7675797
speciesSnowbrush 0.7900657 1.0513415 0.7514834 0.4524286
kingdomBacteria 0.7824899 1.1780848 0.6642051 0.5066169
kingdomFungi -0.1216436 0.9017750 -0.1348935 0.8927063
n_vertices 0.0336583 0.0182490 1.8443884 0.0652382
n_edges -0.0062740 0.0025937 -2.4189740 0.0156314
mean_dist 0.1045359 0.2745054 0.3808154 0.7033708
mean_betweenness -0.0093545 0.0130007 -0.7195376 0.4718733
mean_closeness -0.4507788 1.6083510 -0.2802739 0.7792893
global_effic 0.0709782 0.8650863 0.0820475 0.9346151
clustering_coeficient 0.5004481 0.2923773 1.7116517 0.0870780
max_degree -0.0027581 0.0111646 -0.2470390 0.8048972
speciesSnowbrush:kingdomBacteria -1.9196549 1.3356853 -1.4372060 0.1507777
speciesSnowbrush:kingdomFungi NA NA NA NA
speciesSnowbrush:n_vertices -0.0277443 0.0162003 -1.7125829 0.0869064
speciesSnowbrush:n_edges 0.0056234 0.0022927 2.4526859 0.0142435
speciesSnowbrush:mean_dist -0.1783225 0.2516005 -0.7087527 0.4785404
speciesSnowbrush:mean_betweenness 0.0069343 0.0117019 0.5925841 0.5535102
speciesSnowbrush:mean_closeness 0.0505584 1.5604034 0.0324008 0.9741548
speciesSnowbrush:global_effic -0.2616951 0.7889638 -0.3316946 0.7401461
speciesSnowbrush:clustering_coeficient -0.4328359 0.2784180 -1.5546258 0.1201548
speciesSnowbrush:max_degree 0.0010310 0.0103857 0.0992750 0.9209275
kingdomBacteria:n_vertices -0.0412751 0.0191732 -2.1527432 0.0314290
kingdomFungi:n_vertices -0.0131249 0.0107850 -1.2169553 0.2237297
kingdomBacteria:n_edges 0.0070137 0.0038534 1.8201147 0.0688544
kingdomFungi:n_edges 0.0016993 0.0014452 1.1758683 0.2397532
kingdomBacteria:mean_dist -0.1393771 0.2812262 -0.4956049 0.6202143
kingdomFungi:mean_dist 0.0793556 0.2149002 0.3692673 0.7119580
kingdomBacteria:mean_betweenness 0.0127671 0.0132366 0.9645311 0.3348678
kingdomFungi:mean_betweenness 0.0051542 0.0075743 0.6804893 0.4962542
kingdomBacteria:mean_closeness 0.2616321 1.6248329 0.1610209 0.8720892
kingdomFungi:mean_closeness 0.8705704 1.2202795 0.7134189 0.4756495
kingdomBacteria:global_effic -0.5859759 0.9583746 -0.6114268 0.5409696
kingdomFungi:global_effic 0.1112992 0.6967625 0.1597377 0.8730999
kingdomBacteria:clustering_coeficient -0.0612045 0.3475835 -0.1760857 0.8602401
kingdomFungi:clustering_coeficient -0.3444858 0.2348469 -1.4668530 0.1425348
kingdomBacteria:max_degree 0.0169423 0.0144749 1.1704638 0.2419197
kingdomFungi:max_degree 0.0104688 0.0062428 1.6769499 0.0936703
speciesSnowbrush:kingdomBacteria:n_vertices 0.0342394 0.0190432 1.7979889 0.0722927
speciesSnowbrush:kingdomFungi:n_vertices NA NA NA NA
speciesSnowbrush:kingdomBacteria:n_edges -0.0036401 0.0041559 -0.8758998 0.3811640
speciesSnowbrush:kingdomFungi:n_edges NA NA NA NA
speciesSnowbrush:kingdomBacteria:mean_dist 0.4252445 0.2905229 1.4637210 0.1433889
speciesSnowbrush:kingdomFungi:mean_dist NA NA NA NA
speciesSnowbrush:kingdomBacteria:mean_betweenness -0.0169793 0.0126385 -1.3434610 0.1792379
speciesSnowbrush:kingdomFungi:mean_betweenness NA NA NA NA
speciesSnowbrush:kingdomBacteria:mean_closeness 2.0054281 1.7097727 1.1729209 0.2409331
speciesSnowbrush:kingdomFungi:mean_closeness NA NA NA NA
speciesSnowbrush:kingdomBacteria:global_effic 2.4227245 1.3447266 1.8016483 0.0717145
speciesSnowbrush:kingdomFungi:global_effic NA NA NA NA
speciesSnowbrush:kingdomBacteria:clustering_coeficient -0.6159688 0.4870200 -1.2647710 0.2060648
speciesSnowbrush:kingdomFungi:clustering_coeficient NA NA NA NA
speciesSnowbrush:kingdomBacteria:max_degree -0.0157006 0.0160879 -0.9759266 0.3291900
speciesSnowbrush:kingdomFungi:max_degree NA NA NA NA


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Soil chemistry

Overview of soil properties for each inoculum source:

Testing for significant differences between the samples…

Here are the soil properties that differ significantly between inoculum sources. Sterile inoculum soils are set as the intercept. The stats below pretty nicely reflect the obvious patterns in the overall figure.
term estimate std.error statistic p.value
Mn 1.248 0.268 4.658 0.000
NH4 0.770 0.268 2.875 0.004
Fe:inoc_site1 1.516 0.328 4.618 0.000
K:inoc_site1 0.904 0.328 2.753 0.006
NO3:inoc_site1 -0.793 0.328 -2.417 0.016
TKN:inoc_site1 0.735 0.328 2.240 0.026
Zn:inoc_site1 1.160 0.328 3.536 0.000
Fe:inoc_site2 0.831 0.328 2.532 0.012
K:inoc_site2 0.801 0.328 2.440 0.015
Mn:inoc_site2 -1.081 0.328 -3.294 0.001
TKN:inoc_site2 0.660 0.328 2.010 0.045
Mn:inoc_site3 -1.526 0.328 -4.648 0.000
NH4:inoc_site3 -0.976 0.328 -2.973 0.003
Zn:inoc_site3 -0.693 0.328 -2.112 0.035
C:N:inoc_site4 -0.893 0.328 -2.721 0.007
EC:inoc_site4 -1.026 0.328 -3.127 0.002
Mn:inoc_site4 -1.349 0.328 -4.110 0.000
B:inoc_site5 1.369 0.328 4.171 0.000
Ca:inoc_site5 1.192 0.328 3.631 0.000
K:inoc_site5 0.683 0.328 2.080 0.038
Mg:inoc_site5 0.682 0.328 2.078 0.039
Mn:inoc_site5 -1.099 0.328 -3.350 0.001
NO3:inoc_site5 1.854 0.328 5.649 0.000
TKN:inoc_site5 1.022 0.328 3.114 0.002
Zn:inoc_site5 1.448 0.328 4.412 0.000
B:inoc_site6 0.918 0.328 2.798 0.005
Mn:inoc_site6 -1.535 0.328 -4.678 0.000
NH4:inoc_site6 -0.754 0.328 -2.299 0.022
NO3:inoc_site6 1.273 0.328 3.880 0.000
Zn:inoc_site6 1.290 0.328 3.932 0.000